BioinforMagic: Marrying Galaxy and Bioconductor

Slides for this  training session  at the  2016 Galaxy Community Conference (GCC2016) . R/Bioconductor tools are popular among bioinformaticians for conducting analyses on high-throughput genomics data. Many researchers have written and used their own R/Bioconductor tools but have limited options for sharing their methods with collaborators and ensuring reproducibility of their work. While some R/Bioconductor tools are currently integrated into Galaxy, scientific communities would benefit greatly if a larger repertoire of these tools were available. In this workshop, we will describe the key components of Galaxy tools and outline approaches for integrating R/Bioconductor tools into the Galaxy platform. Workshop attendees will engage in writing their own R/Bioconductor tool and integrating the tool into Galaxy. Additional topics covered in this workshop include wrapping R/Bioconductor tools using Planemo, dealing with R/Bioconductor dependencies, and if time permits interacting with RData objects from within Galaxy using RStudio Galaxy Interactive Environment (GIE). Participants are encouraged to bring in an R-script they want to integrate with Galaxy for the hands on session.